Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi4g142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g143 . . . . . Bpe02g00332 . . . . . . Car09g00308 . . . Cpe06g00255 . . . . . . . Cla05g01617 Cam05g1730 Cec05g1735 Cco05g1791 Clacu05g1719 Cmu05g1603 Cre05g1730 Cone4ag1692 . . . . . . . Blo17g00274 . . . Bpe14g00279 . . Bma02g00338 . . Cmo09g00582 Cma09g00361 . . . . . Bhi09g03092 . . . . . . . . . . . . . . . . Cme07g00188
Vvi4g144 Blo01g01450 Blo12g01027 . Bda03g00130 . . Bma04g00265 . . . Cma01g01705 . . . . . . . . . . . . . Cla05g01618 Cam05g1731 Cec05g1736 Cco05g1792 Clacu05g1720 Cmu05g1604 Cre05g1731 Cone4ag1693 . . . Lsi04g01394 . . . . . . . . Bpe04g00114 . . . Cmo01g01806 . . . Car01g01323 . . Cpe02g00286 Bhi09g03090 . . . . . . . . . . . . . . . . Cme07g00186
Vvi4g145 . . . . . . . . . . . . . Car12g00281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g146 . . . . Bpe02g01556 . . . Cmo05g00427 Cmo12g00250 . . . . . . . Bhi04g01088 . . . . . . . . . . . . . . . Cone17ag0940 Cone20ag0283 . . . . . Blo18g00262 Bda01g01344 Bda13g01302 . . Bma01g00913 . . . . . . . Car05g00351 Cpe11g00355 . . . . . . . . Cla08g00991 Cam08g1437 Cec08g1016 Cco08g1139 Clacu08g1142 . Cre08g0927 Lsi08g00836 . Chy03g01199 .
Vvi4g147 . . . . . . . . . . . . . . . Cpe07g00257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00298 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g148 . . . . Bpe02g01557 . . . . . Cma01g01704 . Car09g00310 . . . Cpe06g00394 . . . . . . . Cla05g01808 . . . . . . . . Cone17ag0941 Cone20ag0284 Lsi04g01391 . . . . . Bda01g01345 . . . Bma01g00912 . . Cmo01g01807 Cmo09g00361 Cma09g00362 . Car01g01322 . . Cpe02g00287 Bhi09g02373 . . . . . . . . . . . . . . . . Cme07g00180
Vvi4g149 . Blo12g01028 . . . . . . . . Cma01g01703 . . . . . . . . . . . . . Cla05g01624 Cam05g1734 Cec05g1742 Cco05g1799 Clacu05g1724 Cmu05g1608 Cre05g1737 . Cone7ag1612 . . Lsi04g01390 . . . . . . . . Bpe04g00113 . . Sed13g1903 Cmo01g01808 . . . Car01g01321 . . Cpe02g00288 Bhi09g03085 Tan01g3468 Cmetu07g0846 . Hepe01g1914 Mch11g0448 . . . . . . . . . . . Cme07g00179
Vvi4g150 . . . . . . . . . Cmo12g00602 . . . Car12g00644 . Cpe07g00577 . Bhi04g01513 Tan02g1585 . . Hepe08g1435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00661 . . . . . . . . . . . Cla08g00988 . . . . . . Lsi08g00832 . Chy03g00656 .
Vvi4g151 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49151506 49154348 - Bda003581.1 Bda01g01344 1344
1 49158843 49166832 - Bda003582.1 Bda01g01345 1345
3 1154182 1156870 - Bda016070.1 Bda03g00130 130
13 35252857 35254056 - Bda000110.1 Bda13g01302 1302
4 26919017 26921833 - XM_039030478.1 Bhi04g01088 1088
4 37677402 37686695 - XM_039029293.1 Bhi04g01513 1513
9 64714318 64723197 - XM_039042063.1 Bhi09g02373 2373
9 79639763 79641321 - XM_039042777.1 Bhi09g03085 3085
9 79739624 79743306 - XM_039041157.1 Bhi09g03090 3090
9 79765329 79771081 - XM_039041296.1 Bhi09g03092 3092
1 53576241 53580110 - BLOR01450 Blo01g01450 1450
12 28161603 28164680 + BLOR05046 Blo12g01027 1027
12 28164977 28166583 + BLOR05047 Blo12g01028 1028
17 2885850 2887593 - BLOR16095 Blo17g00274 274
18 2786909 2799346 + BLOR08750 Blo18g00262 262
1 8841196 8845718 + Bma001141.1 Bma01g00912 912
1 8850907 8854586 + Bma001142.2 Bma01g00913 913
2 5462517 5463869 - Bma014807.1 Bma02g00338 338
4 2189180 2198974 + Bma018717.1 Bma04g00265 265
2 2165494 2171618 - Bpe008173.1 Bpe02g00332 332
2 18577951 18580690 - Bpe009408.1 Bpe02g01556 1556
2 18584317 18589079 - Bpe009409.1 Bpe02g01557 1557
4 787318 788664 - Bpe014835.1 Bpe04g00113 113
4 788930 791610 - Bpe014836.1 Bpe04g00114 114
14 2797902 2799345 + Bpe006932.1 Bpe14g00279 279
5 25840596 25846035 + CaPI482276_05g017300.1 Cam05g1730 1730
5 25849936 25852794 + CaPI482276_05g017310.1 Cam05g1731 1731
5 25906921 25908071 + CaPI482276_05g017340.1 Cam05g1734 1734
8 20708228 20713209 + CaPI482276_08g014370.1 Cam08g1437 1437
1 11818221 11819537 - Carg10716-RA Car01g01321 1321
1 11819931 11824426 + Carg10715-RA Car01g01322 1322
1 11825413 11827214 - Carg10714-RA Car01g01323 1323
5 2024237 2026887 + Carg09308-RA Car05g00351 351
9 1709692 1711307 + Carg02787-RA Car09g00308 308
9 1712584 1716908 - Carg02789-RA Car09g00310 310
12 1853872 1855926 - Carg03888-RA Car12g00281 281
12 4340338 4347958 + Carg17658-RA Car12g00644 644
5 26608999 26614461 + CcPI632755_05g017910.1 Cco05g1791 1791
5 26619947 26622807 + CcPI632755_05g017920.1 Cco05g1792 1792
5 26699296 26700446 + CcPI632755_05g017990.1 Cco05g1799 1799
8 23242332 23245397 + CcPI632755_08g011390.1 Cco08g1139 1139
5 28899987 28904983 + CePI673135_05g017350.1 Cec05g1735 1735
5 28909399 28912260 + CePI673135_05g017360.1 Cec05g1736 1736
5 28974260 28975410 + CePI673135_05g017420.1 Cec05g1742 1742
8 22091048 22094113 + CePI673135_08g010160.1 Cec08g1016 1016
3 9135002 9142025 + Chy3G056360.1 Chy03g00656 656
3 15123967 15126015 - Chy3G061790.1 Chy03g01199 1199
5 26043998 26049450 + ClG42_05g0171900.10 Clacu05g1719 1719
5 26053961 26056822 + ClG42_05g0172000.10 Clacu05g1720 1720
5 26106520 26107670 + ClG42_05g0172400.10 Clacu05g1724 1724
8 21481128 21491040 + ClG42_08g0114200.10 Clacu08g1142 1142
5 27507067 27511993 + ClCG05G015650.1 Cla05g01617 1617
5 27518640 27521801 + ClCG05G015660.1 Cla05g01618 1618
5 27573123 27574595 + ClCG05G015710.1 Cla05g01624 1624
5 29978125 29979155 - ClCG05G017640.1 Cla05g01808 1808
8 22616215 22623204 - ClCG08G009840.2 Cla08g00988 988
8 22666522 22676539 + ClCG08G009870.2 Cla08g00991 991
1 11612451 11614387 - CmaCh01G017030.1 Cma01g01703 1703
1 11614366 11618755 + CmaCh01G017040.1 Cma01g01704 1704
1 11619565 11623127 - CmaCh01G017050.1 Cma01g01705 1705
9 1485295 1488981 + CmaCh09G003610.1 Cma09g00361 361
9 1488485 1493143 - CmaCh09G003620.1 Cma09g00362 362
12 1525123 1527171 - CmaCh12G002980.1 Cma12g00298 298
12 3536318 3544127 + CmaCh12G006610.1 Cma12g00661 661
7 1203549 1205212 - MELO3C016910.2.1 Cme07g00179 179
7 1205933 1209333 + MELO3C016909.2.1 Cme07g00180 180
7 1260419 1264569 - MELO3C016906.2.1 Cme07g00186 186
7 1277550 1279875 - MELO3C016904.2.1 Cme07g00188 188
7 23550536 23552165 + PI0000859.1 Cmetu07g0846 846
1 13267027 13271028 + CmoCh01G018060.1 Cmo01g01806 1806
1 13270753 13276739 - CmoCh01G018070.1 Cmo01g01807 1807
1 13277225 13278583 + CmoCh01G018080.1 Cmo01g01808 1808
5 1987749 1991197 + CmoCh05G004270.1 Cmo05g00427 427
9 1557907 1562263 - CmoCh09G003610.1 Cmo09g00361 361
9 2850373 2859557 - CmoCh09G005820.1 Cmo09g00582 582
12 1623698 1625746 - CmoCh12G002500.1 Cmo12g00250 250
12 3731048 3743267 + CmoCh12G006020.1 Cmo12g00602 602
5 25763379 25768830 + CmPI595203_05g016030.1 Cmu05g1603 1603
5 25773347 25776208 + CmPI595203_05g016040.1 Cmu05g1604 1604
5 25825842 25826992 + CmPI595203_05g016080.1 Cmu05g1608 1608
4 12592297 12593982 + Conep04aG0174600.1 Cone4ag1692 1692
4 12597498 12600678 + Conep04aG0174700.1 Cone4ag1693 1693
7 10959657 10961282 + Conep07aG0166100.1 Cone7ag1612 1612
17 7356084 7358415 - Conep17aG0096700.1 Cone17ag0940 940
17 7364652 7368212 - Conep17aG0096800.1 Cone17ag0941 941
20 1268628 1270509 - Conep20aG0029600.1 Cone20ag0283 283
20 1273239 1276746 - Conep20aG0029700.1 Cone20ag0284 284
2 1478648 1482958 + Cp4.1LG02g05890.1 Cpe02g00286 286
2 1483265 1487831 - Cp4.1LG02g05860.1 Cpe02g00287 287
2 1488318 1489740 + Cp4.1LG02g05900.1 Cpe02g00288 288
6 1364022 1366534 + Cp4.1LG06g02490.1 Cpe06g00255 255
6 2231470 2233236 - Cp4.1LG06g04620.1 Cpe06g00394 394
7 1665689 1668899 - Cp4.1LG07g01830.1 Cpe07g00257 257
7 3855758 3863567 + Cp4.1LG07g05950.1 Cpe07g00577 577
11 1936765 1940385 + Cp4.1LG11g03540.1 Cpe11g00355 355
5 28995321 29000129 + CrPI670011_05g017300.1 Cre05g1730 1730
5 29006684 29009538 + CrPI670011_05g017310.1 Cre05g1731 1731
5 29066758 29067906 + CrPI670011_05g017370.1 Cre05g1737 1737
8 22473180 22476258 + CrPI670011_08g009270.1 Cre08g0927 927
1 83946689 83947946 + Hsped.01g19140.1 Hepe01g1914 1914
8 17207470 17215915 - Hsped.08g14350.1 Hepe08g1435 1435
4 21720928 21722463 - Lsi04G013900.1 Lsi04g01390 1390
4 21723598 21729571 + Lsi04G013910.1 Lsi04g01391 1391
4 21742514 21746271 - Lsi04G013940.1 Lsi04g01394 1394
8 16752332 16759824 + Lsi08G008320.1 Lsi08g00832 832
8 16804463 16814757 + Lsi08G008360.1 Lsi08g00836 836
11 2802838 2804760 + MC11g0361 Mch11g0448 448
13 23980493 23984020 + Sed0027665.1 Sed13g1903 1903
1 99970097 99971784 + Tan0015562.1 Tan01g3468 3468
2 73167821 73174697 + Tan0019178.4 Tan02g1585 1585
4 1328146 1329643 + Vvi4g142 Vvi4g142 142
4 1336305 1338118 + Vvi4g143 Vvi4g143 143
4 1350184 1354369 + Vvi4g144 Vvi4g144 144
4 1354827 1355199 + Vvi4g145 Vvi4g145 145
4 1355370 1359837 - Vvi4g146 Vvi4g146 146
4 1365800 1369920 - Vvi4g147 Vvi4g147 147
4 1376490 1381817 - Vvi4g148 Vvi4g148 148
4 1382337 1384647 + Vvi4g149 Vvi4g149 149
4 1391338 1403082 - Vvi4g150 Vvi4g150 150
4 1403977 1408138 + Vvi4g151 Vvi4g151 151
       

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